RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11902
(336 letters)
>gnl|CDD|143642 cd07882, RHD-n_TonEBP, N-terminal sub-domain of the Rel homology
domain (RHD) of tonicity-responsive enhancer binding
protein (TonEBP). Proteins containing the Rel homology
domain (RHD) are metazoan transcription factors. The RHD
is composed of two structural sub-domains; this model
characterizes the N-terminal RHD sub-domain of the
tonicity-responsive enhancer binding protein (TonEBP),
also called NFAT5. Mammalian TonEBP regulates the
expression of genes in response to tonicity. It plays a
pivotal role in urinary concentrating mechanisms in
kidney medulla, by triggering the accumulation of
osmolytes that enable renal medullary cells to tolerate
high levels of urea and salt.
Length = 161
Score = 251 bits (642), Expect = 4e-84
Identities = 90/163 (55%), Positives = 115/163 (70%), Gaps = 4/163 (2%)
Query: 93 LEITSQPEQQHRARYQTEGSRGAVKDKSGNGFPVVKLVGYNGPATLEVFIGTDQGKIAPH 152
L+I QPE QHRARY TEGSRG+VKD+S GFP VKL GYN P L+VF+GTD G++ PH
Sbjct: 3 LKILVQPETQHRARYLTEGSRGSVKDRSQQGFPTVKLEGYNKPVVLQVFVGTDSGRVKPH 62
Query: 153 MFYQACRVAGKNSTPCLEKKTDGTVIIDIDFDPSKDMSVTCDCVGILKERNVDVEQRFPE 212
FYQAC+V G+N+TPC E +GT +I++ DP+ +M+++ DCVGILK RN DVE R
Sbjct: 63 GFYQACKVTGRNTTPCEEVDVEGTTVIEVPLDPTNNMTISVDCVGILKLRNADVEARIGI 122
Query: 213 DSSAKNKKRSTRCRMVFRTTIIHPGTRETEVLQVASHPIMCNQ 255
A++KK+STR R+VFR I T LQ S+PI+C Q
Sbjct: 123 ---ARSKKKSTRVRLVFRVIIPRKDG-STLTLQTVSNPILCTQ 161
>gnl|CDD|143648 cd07927, RHD-n_NFAT_like, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of activated T-cells
(NFAT) proteins and similar proteins. Proteins
containing the Rel homology domain (RHD) are metazoan
transcription factors. The RHD is composed of two
structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the NFAT family of
transcription factors. NFAT transcription complexes are
a target of calcineurin, a calcium dependent
phosphatase, and activate genes that are mainly involved
in cell-cell interaction. Upon de-phosphorylation of the
nuclear localization signal, NFAT enters the nucleus and
acts as a transcription factor; its export from the
nucleus is triggered by phosphorylation via export
kinases. NFATs play important roles in mediating the
immune response, and are found in T cells, B Cells, NK
cells, mast cells, and monocytes. NFATs are also found
in various non-hematopoietic cell types, where they play
roles in development. This group also contains the
N-terminal RHD sub-domain of the non-calcium regulated
tonicity-responsive enhancer binding protein (TonEBP),
also called NFAT5. Mammalian TonEBP regulates the
expression of genes in response to tonicity. It plays a
pivotal role in urinary concentrating mechanisms in
kidney medulla, by triggering the accumulation of
osmolytes that enable renal medullary cells to tolerate
high levels of urea and salt.
Length = 161
Score = 172 bits (438), Expect = 2e-53
Identities = 84/163 (51%), Positives = 102/163 (62%), Gaps = 4/163 (2%)
Query: 93 LEITSQPEQQHRARYQTEGSRGAVKDKSGNGFPVVKLVGYNGPATLEVFIGTDQGKIAPH 152
L I QPE HRARY+TEGSRGAVK S GFP VKL GY P L+VFIGT G++ PH
Sbjct: 3 LRIEVQPEPHHRARYETEGSRGAVKAPSTGGFPTVKLHGYMEPVGLQVFIGTASGRLKPH 62
Query: 153 MFYQACRVAGKNSTPCLEKKTDGTVIIDIDFDPSKDMSVTCDCVGILKERNVDVEQRFPE 212
FYQ R+ GK +TPC EK T +++I +P +M+ T DC GILK RN D+E R E
Sbjct: 63 AFYQVHRITGKTTTPCKEKIIGNTKVLEIPLEPKNNMTATIDCAGILKLRNADIELRKGE 122
Query: 213 DSSAKNKKRSTRCRMVFRTTIIHPGTRETEVLQVASHPIMCNQ 255
KK++TR R+VFR I R LQ AS+PI C+Q
Sbjct: 123 TDI---KKKNTRARLVFRVHIPEKDGRIVS-LQTASNPIECSQ 161
>gnl|CDD|143641 cd07881, RHD-n_NFAT, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of activated T-cells
(NFAT) proteins. Proteins containing the Rel homology
domain (RHD) are metazoan transcription factors. The RHD
is composed of two structural sub-domains; this model
characterizes the N-terminal RHD sub-domain of the NFAT
family of transcription factors. NFAT transcription
complexes are a target of calcineurin, a calcium
dependent phosphatase, and activate genes that are
mainly involved in cell-cell interaction. Upon
de-phosphorylation of the nuclear localization signal,
NFAT enters the nucleus and acts as a transcription
factor; its export from the nucleus is triggered by
phosphorylation via export kinases. NFATs play important
roles in mediating the immune response, and are found in
T cells, B Cells, NK cells, mast cells, and monocytes.
NFATs are also found in various non-hematopoietic cell
types, where they play roles in development.
Length = 175
Score = 152 bits (385), Expect = 3e-45
Identities = 80/168 (47%), Positives = 98/168 (58%), Gaps = 11/168 (6%)
Query: 93 LEITSQPEQQHRARYQTEGSRGAVKDKSGNGFPVVKLVGYNG--PATLEVFIGT-DQGKI 149
L I QP+ HRA Y+TEGSRGAVK +G G PVV+L GY P TL++FIGT D +
Sbjct: 13 LRIEVQPKPHHRAHYETEGSRGAVKASTG-GHPVVQLHGYMENKPLTLQMFIGTADDRYL 71
Query: 150 APHMFYQACRVAGKN-STPCLEKKTDGTVIIDIDFDPSKDMSVTCDCVGILKERNVDVEQ 208
PH FYQ R+ GK +T E T +++I P +M + DC GILK RN D+E
Sbjct: 72 RPHAFYQVHRITGKTVATASQEIIISNTKVLEIPLLPENNMRASIDCAGILKLRNSDIEL 131
Query: 209 RFPE-DSSAKNKKRSTRCRMVFRTTIIHPGTRETEVLQVASHPIMCNQ 255
R E D KN TR R+VFR I P R LQVAS+PI C+Q
Sbjct: 132 RKGETDIGRKN----TRVRLVFRVHIPQPSGR-VLSLQVASNPIECSQ 174
>gnl|CDD|201301 pfam00554, RHD, Rel homology domain (RHD). Proteins containing the
Rel homology domain (RHD) are eukaryotic transcription
factors. The RHD is composed of two structural domains.
This is the N-terminal domain that is similar to that
found in P53. The C-terminal domain has an
immunoglobulin-like fold (See pfam01833) that binds to
DNA.
Length = 169
Score = 120 bits (303), Expect = 4e-33
Identities = 46/183 (25%), Positives = 74/183 (40%), Gaps = 35/183 (19%)
Query: 93 LEITSQPEQQ-HRARYQTEG-SRGAVKD----KSGNGFPVVKLVGYNGPATLEVFIGTDQ 146
LEI QP+Q+ R RY+ EG S G++ +S FP V++ Y+GPA + V + T
Sbjct: 1 LEIVEQPKQRGMRFRYKCEGRSAGSIPGESSTRSKKTFPTVQICNYDGPAVIRVSLVTKD 60
Query: 147 GKIAPHMFYQACRVAGKNSTPCLEKKTDGTVIIDIDFDPSKDMSVTCDCVGILKERNVDV 206
PH + GK+ DG + +++ P +DM + +GI + DV
Sbjct: 61 EPHRPH----PHSLVGKDC-------KDG--VCEVELGP-EDMVASFQNLGIQCVKKKDV 106
Query: 207 EQRFPEDSSAKNKKRS--------------TRCRMVFRTTIIHP-GTRETEVLQVASHPI 251
E+ E + R+ F+ + G T + V S+PI
Sbjct: 107 EEALKERIELNIDPFNVGFEALRQIKDMDLNVVRLCFQAFLPDTRGNFTTPLPPVVSNPI 166
Query: 252 MCN 254
Sbjct: 167 YDK 169
>gnl|CDD|143640 cd07827, RHD-n, N-terminal sub-domain of the Rel homology domain
(RHD). Proteins containing the Rel homology domain
(RHD) are metazoan transcription factors. The RHD is
composed of two structural sub-domains; this model
characterizes the N-terminal sub-domain, which may be
distantly related to the DNA-binding domain found in
P53. The C-terminal sub-domain has an
immunoglobulin-like fold and serves as a dimerization
module that also binds DNA (see cd00102). The RHD is
found in NF-kappa B, nuclear factor of activated T-cells
(NFAT), the tonicity-responsive enhancer binding protein
(TonEBP), and the arthropod proteins Dorsal and Relish
(Rel).
Length = 174
Score = 106 bits (267), Expect = 6e-28
Identities = 50/185 (27%), Positives = 75/185 (40%), Gaps = 33/185 (17%)
Query: 92 YLEITSQPEQQ-HRARYQTEG-SRGAVKDKSGN----GFPVVKLVGYNGPATLEVFIGTD 145
YLEIT QP+Q+ HR RY+ EG S G++ ++ FP VKL YNGPA + V + T
Sbjct: 2 YLEITEQPKQRGHRFRYECEGRSAGSIPGENSTADRKTFPTVKLRNYNGPAKIVVSLVTK 61
Query: 146 QGKIAPHMFYQACRVAGKNSTPCLEKKTDGTVIIDIDFDPSKDMSVTCDCVGILKERNVD 205
PH +Q C + + ++ P +M+ + + +GI R D
Sbjct: 62 DDPPKPHP-HQLVGKTD-----CRDG------VCEVRLGPKNNMTASFNNLGIQCVRKKD 109
Query: 206 VEQR--------------FPEDSSAKNKKRSTRCRMVFRTTIIHPGTRETEVL-QVASHP 250
VE+ + R R+ F+ I T L V S+P
Sbjct: 110 VEEALGQRIQLGIDPFMVHKGPEGNASDIDLNRVRLCFQAFIEDSDGGFTLPLPPVLSNP 169
Query: 251 IMCNQ 255
I +
Sbjct: 170 IYDKK 174
>gnl|CDD|238583 cd01178, IPT_NFAT, IPT domain of the NFAT family of transcription
factors. NFAT transcription complexes are a target of
calcineurin, a calcium dependent phosphatase, and
activate genes mainly involved in cell-cell-interaction.
Length = 101
Score = 67.9 bits (166), Expect = 2e-14
Identities = 33/79 (41%), Positives = 38/79 (48%), Gaps = 21/79 (26%)
Query: 259 VPEICKKSLTSCPVTGGAELFKVSPTDTIAGKGLLQDHPDAILGKNFLKDTQVKFQKMVA 318
+PEI KKSL SC V GG ELF + GKNFLKD++V FQ+
Sbjct: 1 LPEIEKKSLNSCSVNGGEELF--------------------LTGKNFLKDSKVVFQEKGQ 40
Query: 319 DIC-QWEESVLPDKEFLQQ 336
D QWE DKE Q
Sbjct: 41 DGEAQWEAEATIDKEKSHQ 59
>gnl|CDD|238336 cd00602, IPT_TF, IPT domain of eukaryotic transcription factors
NF-kappaB/Rel, nuclear factor of activated Tcells
(NFAT), and recombination signal J-kappa binding
protein (RBP-Jkappa). The IPT domains in these proteins
are involved in DNA binding. Most NF-kappaB/Rel proteins
form homo- and heterodimers, while NFAT proteins are
largely monomeric (with TonEBP being an exception).
While the majority of sequence-specific DNA binding
elements are found in the N-terminal domain, several are
found in the IPT domain in loops adjacent to, and
including, the linker region.
Length = 101
Score = 48.8 bits (117), Expect = 1e-07
Identities = 18/78 (23%), Positives = 27/78 (34%), Gaps = 21/78 (26%)
Query: 260 PEICKKSLTSCPVTGGAELFKVSPTDTIAGKGLLQDHPDAILGKNFLK-DTQVKFQKMVA 318
IC+ S S V GG E+F +L K D +V F +
Sbjct: 1 LPICRVSSLSGSVNGGDEVF--------------------LLCDKVNKPDIKVWFGEKGP 40
Query: 319 DICQWEESVLPDKEFLQQ 336
WE + +E ++Q
Sbjct: 41 GETVWEAEAMFRQEDVRQ 58
>gnl|CDD|143643 cd07883, RHD-n_NFkB, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of kappa light
polypeptide gene enhancer in B-cells (NF-kappa B).
Proteins containing the Rel homology domain (RHD) are
metazoan transcription factors. The RHD is composed of
two structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the NF-kappa B1 and B2
families of transcription factors, also referred to as
class I members of the NF-kappa B family. In class I
NF-kappa Bs, the RHD domain co-occurs with C-terminal
ankyrin repeats. Family members include NF-kappa B1 and
NF-kappa B2. NF-kappa B1 is commonly referred to as p105
or p50 (proteolytically processed form), while NF-kappa
B2 is called p100 or p52 (proteolytically processed
form). NF-kappa B proteins are part of a protein complex
that acts as a transcription factor, which is
responsible for regulating a host of cellular responses
to a variety of stimuli. This complex tightly regulates
the expression of a large number of genes, and is
involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and REL). p105 and p100 may also act as I-kappa Bs due
to their C-terminal ankyrin repeats.
Length = 197
Score = 47.9 bits (114), Expect = 1e-06
Identities = 36/115 (31%), Positives = 51/115 (44%), Gaps = 20/115 (17%)
Query: 91 VYLEITSQPEQQ-HRARYQTEGSR-----GAVKDKSGNGFPVVKLVGYNGPATLEVFIGT 144
YLEI QP+Q+ R RY EG GA +K+ +P VK+ Y GPA + V + T
Sbjct: 1 PYLEILEQPKQRGFRFRYGCEGPSHGGLPGASSEKNKKSYPTVKICNYQGPARIVVQLVT 60
Query: 145 DQGKIAPHMFYQACRVAGKNSTPCLEKKTDGTVIIDIDFDPSKDMSVTCDCVGIL 199
+ H A + GK+ DG + + KDM+ +GIL
Sbjct: 61 NSEPPRLH----AHSLVGKHC-------EDGICTVQVG---PKDMTAQFPNLGIL 101
>gnl|CDD|143647 cd07887, RHD-n_Dorsal_Dif, N-terminal sub-domain of the Rel
homology domain (RHD) of the arthropod protein Dorsal.
Proteins containing the Rel homology domain (RHD) are
metazoan transcription factors. The RHD is composed of
two structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the arthropod Dorsal and
Dif (Dorsal-related immunity factor), and similar
proteins. Dorsal and Dif are Rel-like transcription
factors, which play roles in mediating innate immunity
in Drosophila. They are activated via the Toll pathway.
Cytoplasmic Dorsal/Dif are inactivated via forming a
complex with Cactus, the Drosophila homologue of
mammalian I-kappa B proteins. In response to signals,
Cactus is degraded and Dorsal/Dif can be transported
into the nucleus, where they act as transcription
factors. Dorsal is also an essential gene in
establishing the proper dorsal/ventral polarity in the
developing embryo.
Length = 173
Score = 41.7 bits (98), Expect = 1e-04
Identities = 42/176 (23%), Positives = 64/176 (36%), Gaps = 24/176 (13%)
Query: 92 YLEITSQPEQQH-RARYQTEGSR-----GAVKDKSGNGFPVVKLVGYNGPATLEVFIGTD 145
Y+ I QP + R RY+ EG GA G FP +++V Y+G A + V T
Sbjct: 2 YVRIVEQPTSRALRFRYECEGRSAGSIPGANSTSEGKTFPTIQVVNYDGRAVVVVSCVTK 61
Query: 146 QGKIAPHMFYQACRVAGKNSTPCLEKKTDGTVI----IDIDFDPSKDMSVTCDCVGILKE 201
PH + K + I + I KD+ + + + +E
Sbjct: 62 DEPFRPHPHNLVGKEGCKKGVCTKKINPTEMRIVFQKLGIQCVKKKDVE---ESLKLREE 118
Query: 202 RNVDVEQRFPEDSSAKNKKRSTR-----CRMVFRTTIIHPGTRETEVLQ-VASHPI 251
NVD P + +K + R+ F+ + R T L V S PI
Sbjct: 119 INVD-----PFRTGFDHKDQINSIDLNVVRLCFQVFLEDENGRFTVPLPPVVSDPI 169
>gnl|CDD|143651 cd07935, RHD-n_NFkB1, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor of kappa B1 (NF-kappa
B1). Proteins containing the Rel homology domain (RHD)
are metazoan transcription factors. The RHD is composed
of two structural sub-domains; this model characterizes
the N-terminal RHD sub-domain of the NF-kappa B1 family
of transcription factors, a class I member of the
NF-kappa B family. In class I NF-kappa Bs, the RHD
domain co-occurs with C-terminal ankyrin repeats.
NF-kappa B1 is commonly referred to as p105 or p50
(proteolytically processed form). NF-kappa B proteins
are part of a protein complex that acts as a
transcription factor, which is responsible for
regulating a host of cellular responses to a variety of
stimuli. This complex tightly regulates the expression
of a large number of genes, and is involved in processes
such as adaptive and innate immunity, stress response,
inflammation, cell adhesion, proliferation and
apoptosis. The cytosolic NF-kappa B complex is activated
via phosphorylation of the ankyrin-repeat containing
inhibitory protein I-kappa B, which dissociates from the
complex and exposes the nuclear localization signal of
the heterodimer (NF-kappa B and REL). NF-kappa B1 is
involved in the canonical NF-kappa B signaling pathway
which is activated by many agonists and is essential in
immune and inflammatory responses, as well as cell
survival. p105 is involved in its own specific NF-kappa
B signaling pathway which is also implicated in immune
and inflammatory responses. p105 may also act as an
I-kappa B due to its C-terminal ankyrin repeats. It is
also involved in mitogen-activated protein kinase (MAPK)
signaling as its degradation leads to the activation of
TPL-2, a MAPK kinase kinase which activates ERK
pathways.
Length = 202
Score = 41.0 bits (96), Expect = 3e-04
Identities = 37/114 (32%), Positives = 51/114 (44%), Gaps = 20/114 (17%)
Query: 92 YLEITSQPEQQ-HRARYQTEGSR-----GAVKDKSGNGFPVVKLVGYNGPATLEVFIGTD 145
YL+I QP+Q+ R RY EG GA +K+ +P VK+ Y GPA + V + T+
Sbjct: 2 YLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTN 61
Query: 146 QGKIAPHMFYQACRVAGKNSTPCLEKKTDGTVIIDIDFDPSKDMSVTCDCVGIL 199
I H A + GK+ DG + KDM V +GIL
Sbjct: 62 GKNIHLH----AHSLVGKHC-------EDGICTVTAG---PKDMVVGFANLGIL 101
>gnl|CDD|143644 cd07884, RHD-n_Relish, N-terminal sub-domain of the Rel homology
domain (RHD) of the arthropod protein Relish. Proteins
containing the Rel homology domain (RHD) are metazoan
transcription factors. The RHD is composed of two
structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the arthropod Relish
protein, in which the RHD domain co-occurs with
C-terminal ankyrin repeats. Family members are sometimes
referred to as p110 or p68 (proteolytically processed
form). Relish is an NF-kappa B-like transcription
factor, which plays a role in mediating innate immunity
in Drosophila. It is activated via the Imd (immune
deficiency) pathway, which triggers phosphorylation of
Relish. IKK-dependent proteolytic cleavage of Relish
(which involves Dredd) results in a smaller active form
(without the C-terminal ankyrin repeats), which is
transported into the nucleus and functions as a
transactivator.
Length = 159
Score = 39.3 bits (92), Expect = 7e-04
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 92 YLEITSQPEQQHRARYQTE--GSRGAVK----DKSGNGFPVVKLVGYNGPATLEVFIGT- 144
+L I QP + R RY++E G+ G++ S FP VKL Y G A + +
Sbjct: 2 FLRIVEQPVDKFRFRYKSEMHGTHGSLLGERSTSSKKTFPTVKLCNYRGQAVIRCSLYQA 61
Query: 145 DQGKIAPH 152
D + PH
Sbjct: 62 DDNRRKPH 69
>gnl|CDD|143650 cd07934, RHD-n_NFkB2, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor kappa B2 (NF-kappa B2).
Proteins containing the Rel homology domain (RHD) are
metazoan transcription factors. The RHD is composed of
two structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the NF-kappa B2 family of
transcription factors, a class I member of the NF-kappa
B family. In class I NF-kappa Bs, the RHD domain
co-occurs with C-terminal ankyrin repeats. NF-kappa B2
is commonly referred to as p100 or p52 (proteolytically
processed form). NF-kappa B proteins are part of a
protein complex that acts as a transcription factor,
which is responsible for regulating a host of cellular
responses to a variety of stimuli. This complex tightly
regulates the expression of a large number of genes, and
is involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and REL). NF-kappa B2 is involved in the alternative
NF-kappa B signaling pathway which is activated by few
agonists and plays an important role in secondary
lymphoid organogenesis, maturation of B-cells, and
adaptive humoral immunity. p100 may also act as an
I-kappa B due to its C-terminal ankyrin repeats.
Length = 185
Score = 39.1 bits (91), Expect = 0.001
Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 92 YLEITSQPEQQ-HRARYQTEGSR-----GAVKDKSGNGFPVVKLVGYNGPATLEV 140
YL I QP+Q+ R RY EG GA +K +P VK+ Y G A +EV
Sbjct: 2 YLVIIEQPKQRGFRFRYVCEGPSHGGLPGASSEKGRKTYPTVKICNYVGMARIEV 56
>gnl|CDD|143645 cd07885, RHD-n_RelA, N-terminal sub-domain of the Rel homology
domain (RHD) of RelA. Proteins containing the Rel
homology domain (RHD) are metazoan transcription
factors. The RHD is composed of two structural
sub-domains; this model characterizes the N-terminal RHD
domain of the RelA family of transcription factors,
categorized as a class II member of the NF-kappa B
family. In class II NF-kappa Bs, the RHD domain
co-occurs with a C-terminal transactivation domain
(TAD). NF-kappa B proteins are part of a protein complex
that acts as a transcription factor, which is
responsible for regulating a host of cellular responses
to a variety of stimuli. This complex tightly regulates
the expression of a large number of genes, and is
involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and Rel). RelA (also called p65) forms heterodimers
with NF-kappa B1 (p50) and B2 (p52). RelA also forms
homodimers.
Length = 169
Score = 33.3 bits (76), Expect = 0.086
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 92 YLEITSQPEQQ-HRARYQTEG-SRGAVKDKSGNG----FPVVKLVGYNGPATLEVFIGTD 145
Y+EI QP+Q+ R RY+ EG S G++ + P +K+ Y GP + + + T
Sbjct: 2 YVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINNYTGPGRVRISLVTK 61
Query: 146 QGKIAPH 152
PH
Sbjct: 62 DPPHKPH 68
>gnl|CDD|235650 PRK05939, PRK05939, hypothetical protein; Provisional.
Length = 397
Score = 30.8 bits (70), Expect = 0.94
Identities = 30/105 (28%), Positives = 43/105 (40%), Gaps = 28/105 (26%)
Query: 202 RNVDVEQRFPEDSSAKNKKRSTR--CRMVFRTTIIHPGTRETEVLQVASHPIMCNQPPGV 259
R + VE + + +N + R RMVF TI +PGT QVA G+
Sbjct: 107 RGLGVEVTMVDATDVQNVAAAIRPNTRMVFVETIANPGT------QVADL-------AGI 153
Query: 260 PEICKK---------SLTSC----PVTGGAELFKVSPTDTIAGKG 291
+C++ ++TS P GA L S + IAG G
Sbjct: 154 GALCRERGLLYVVDNTMTSPWLFRPKDVGASLVINSLSKYIAGHG 198
>gnl|CDD|214897 smart00900, FMN_bind, This conserved region includes the
FMN-binding site of the NqrC protein as well as the NosR
and NirI regulatory proteins.
Length = 86
Score = 27.3 bits (61), Expect = 3.5
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 131 GYNGPATLEVFIGTDQGKIA 150
GY GP T+ V + D+GKI
Sbjct: 1 GYGGPITVLVTVKDDKGKIT 20
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 29.1 bits (66), Expect = 3.5
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 180 DIDFDPSKDMSVTCD-CVGILKERNVDV 206
D D P+ D+ + C I++ R+VDV
Sbjct: 76 DGDGGPTIDLCGVGEHCQAIMEGRHVDV 103
>gnl|CDD|199860 cd06236, M14_AGBL5_like, Peptidase M14-like domain of ATP/GTP
binding protein (AGBL)-5 and related proteins.
Peptidase M14-like domain of ATP/GTP binding
protein_like (AGBL)-5, and related proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This eukaryotic subgroup includes the human
AGBL5 and the mouse cytosolic carboxypeptidase (CCP)-5.
ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins
are active metallopeptidases that are thought to act on
cytosolic proteins such as alpha-tubulin, to remove a
C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause
Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however
does not belong to this subgroup. AGTPBP-1/Nna1-like
proteins from the different phyla are highly diverse,
but they all contain a unique N-terminal conserved
domain right before the CP domain. It has been suggested
that this N-terminal domain might act as a folding
domain.
Length = 308
Score = 28.5 bits (64), Expect = 4.7
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 194 DCVGILKERNVDVEQRFPEDSSAKNKKRSTRCRMVFRTTIIHPGTRET 241
C G+L+ER + FP+ S+ + + + + R+ F ++ +HPG ET
Sbjct: 37 SCHGLLEEREPRLPGLFPDRSTPRPFRFTGK-RVFFLSSRVHPG--ET 81
>gnl|CDD|238050 cd00102, IPT, Immunoglobulin-like fold, Plexins, Transcription
factors (IPT). IPTs are also known as Transcription
factor ImmunoGlobin (TIG) domains. They are present in
intracellular transcription factors, cell surface
receptors (such as plexins and scatter factor
receptors), as well as, cyclodextrin glycosyltransferase
and similar enzymes. Although they are involved in DNA
binding in transcription factors, their function in
other proteins is unknown. In these transcription
factors, IPTs form homo- or heterodimers with the
exception of the nuclear factor of activated Tcells
(NFAT) transcription factors which are mainly monomers.
Length = 89
Score = 26.7 bits (59), Expect = 5.7
Identities = 14/54 (25%), Positives = 19/54 (35%), Gaps = 18/54 (33%)
Query: 260 PEICKKSLTSCPVTGGAELFKVSPTDTIAGKGLLQDHPDAILGKNFLKDTQVKF 313
P I S +S PV+GG E+ TI G + +V F
Sbjct: 1 PVITSISPSSGPVSGGTEV-------TITGSNF-----------GSGSNLRVTF 36
>gnl|CDD|233876 TIGR02464, ribofla_fusion, conserved hypothetical protein,
ribA/ribD-fused. This model describes a sequence region
that occurs in at least three different polypeptide
contexts. It is found fused to GTP cyclohydrolase II,
the RibA of riboflavin biosynthesis (TIGR00505), as in
Vibrio vulnificus. It is found fused to riboflavin
biosynthesis protein RibD (TIGR00326) in rice and
Arabidopsis. It occurs as a standalone protein in a
number of bacterial species in varied contexts,
including single gene operons and bacteriophage genomes.
The member from E. coli currently is named YbiA. The
function(s) of members of this family is unknown.
Length = 153
Score = 27.3 bits (61), Expect = 7.2
Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 273 TGGAELFKVSPTDTIAGKGL---LQDHPDAILGKNFL 306
TGG +L + SP D I G GL P GKN L
Sbjct: 105 TGGKKLVEASPNDKIWGIGLDAQDARIPRNWKGKNLL 141
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 27.4 bits (62), Expect = 7.6
Identities = 17/70 (24%), Positives = 24/70 (34%), Gaps = 29/70 (41%)
Query: 64 RRLYGKRLSNITAQNSASISYSVRDPSVYLE-ITSQPEQQHRARYQTEGSRGAVKDKSGN 122
RRL +R++ + + LE + Q E Q R +
Sbjct: 8 RRLIRERIAKLRKE---------------LEKVKKQRELQRARR-------------KRS 39
Query: 123 GFPVVKLVGY 132
G P V LVGY
Sbjct: 40 GVPTVALVGY 49
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 28.3 bits (64), Expect = 8.1
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 168 CLEKKTDGTVIIDIDFDPSKDMSVTCD-CVG 197
C + DG + I++ F P D+ V C+ C G
Sbjct: 733 CEACQGDGVIKIEMHFLP--DVYVPCEVCHG 761
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.132 0.399
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,647,528
Number of extensions: 1524396
Number of successful extensions: 1062
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1035
Number of HSP's successfully gapped: 22
Length of query: 336
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 239
Effective length of database: 6,635,264
Effective search space: 1585828096
Effective search space used: 1585828096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)